3VK7

Crystal structure of DNA-glycosylase bound to DNA containing 5-Hydroxyuracil

Summary for 3VK7

• Entry DOI: 10.2210/pdb3vk7/pdb
• Related: 3A46 3VK8
• Descriptor: Probable formamidopyrimidine-DNA glycosylase, DNA (5'-D(*GP*TP*AP*GP*AP*CP*GP*TP*GP*GP*AP*CP*G)-3'), DNA (5'-D(*CP*GP*TP*CP*CP*AP*(OHU)P*GP*TP*CP*TP*AP*C)-3'), ... (5 entities in total)
• Functional Keywords: dna glycosylase, hneil1 ortholog, dna lesion, 5-hydroxyuracil, zincless finger, dna binding, hydrolase-dna complex, hydrolase/dna
• Biological source: Acanthamoeba polyphaga mimivirus (APMV)
• Total number of polymer chains: 6
• Total formula weight: 85177.12

Authors

Imamura, K.,Averill, A.,Wallace, S.S.,Doublie, S. (deposition date: 2011-11-10, release date: 2011-12-14, Last modification date: 2023-11-08)

Primary citation

Imamura, K.,Averill, A.,Wallace, S.S.,Doublie, S.
Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA
J.Biol.Chem., 287:4288-4298, 2012

PubMed Abstract: Thymine glycol (Tg) and 5-hydroxyuracil (5-OHU) are common oxidized products of pyrimidines, which are recognized and cleaved by two DNA glycosylases of the base excision repair pathway, endonuclease III (Nth) and endonuclease VIII (Nei). Although there are several structures of Nei enzymes unliganded or bound to an abasic (apurinic or apyrimidinic) site, until now there was no structure of an Nei bound to a DNA lesion. Mimivirus Nei1 (MvNei1) is an ortholog of human NEIL1, which was previously crystallized bound to DNA containing an apurinic site (Imamura, K., Wallace, S. S., and Doublié, S. (2009) J. Biol. Chem. 284, 26174-26183). Here, we present two crystal structures of MvNei1 bound to two oxidized pyrimidines, Tg and 5-OHU. Both lesions are flipped out from the DNA helix. Tg is in the anti conformation, whereas 5-OHU adopts both anti and syn conformations in the glycosylase active site. Only two protein side chains (Glu-6 and Tyr-253) are within hydrogen-bonding contact with either damaged base, and mutating these residues did not markedly affect the glycosylase activity. This finding suggests that lesion recognition by Nei occurs before the damaged base flips into the glycosylase active site.

PubMed: 22170059
DOI: 10.1074/jbc.M111.315309

Experimental method

X-RAY DIFFRACTION (2.1 Å)